IUPMStats v1.0

Infection Frequency Calculator

Use this calculator to estimate infection frequencies from limiting dilution assays. In particular, this calculator can be used with an outgrowth assay to measure latent infection in HIV 1, 2. Enter information about your wells in the following order, using a separate line for each well size: number of cells per well, number of replicates of this size, and number of positive outcomes (i.e., wells in which outgrowth was detected). In addition to providing a maximum-likelihood estimate, this calculator returns a 95% confidence interval. Further information about interpreting the output is provided under "About this Calculator."

Enter well size (# cells), Number of replicates for this size, Number of positive outcomes for this size

Enter Number of Unique Well Sizes, Maximum Well Size (# cells), and Dilution Factor

Enter well size (# cells), Number of replicates for this size, Number of positive outcomes for this size

Choose a Text File to Upload:

Or Paste Data:

To upload data for a single patient, create a text file where each row has three numbers: the well size (# cells), the number of replicates for this size, and the number of positive outcomes for this size. The values may be delimited by either white space or commas. For example, your file could look like this:

900,9,1
400,5,2
100,10,2

For multiple patients, simply add rows with a greater-than sign followed by the patient name (in homage to fasta format). For example,

In this mode, the app will produce a graph showing the infection frequencies (IUPM) across the set of patients.

Maximum likelihood

Output Data

About This Calculator

To measure the frequency of HIV-1 latency, The Siliciano Lab developed an assay some years ago that uses uninfected donor cells to grow HIV-1 out of cells from infected patients at various dilutions1, 2. This calculator, written by Daniel Rosenbloom and made into a web app by Oliver Elliott, computes the frequency of latent infection based on which dilutions of patient cells are positive for HIV-1 growth.

Interpreting the Output Statistics

The maximum likelihood estimate and confidence interval provide a good estimate of the infection frequency, assuming that (1) many cells (>100s) are used in the assay, and (2) each cell in each well has the same probability of being infected.

The p-value can be used to detect very strange, or unlikely, results in the limiting dilution assay. For instance, if several large wells are negative but several small wells are positive, the resulting p-value will be very low, indicating that there may have been cross-contamination, improper labeling of wells, insufficiently mixed cells, or another failure of the assay. (Frequent users of this calculator should note: Every 100 assays that you run, you should expect to see a p-value below 0.01, just by chance!)

For all-negative well outcomes, the maximum likelihood estimate is formally zero. To provide more useful information, a posterior median estimate is given instead. This value reports the median of the Bayesian posterior distribution, using a uniform prior. If you had a reasonable prior belief that your assay could turn up at least one positive well, then this is a decent rough estimate. A higher bound is also provided, at the 95th percentile of the posterior distribution; this is a good upper bound. The p-value is not a meaningful output in this case, so it is not shown.

If you have all-positive assay results, then close this app and use smaller wells!

Functionality

This calculator features three ways to input data. The "Custom Well Sizes" pane allows you to input data with maximum flexibility. The "Constant Limiting Dilution" pane, on the other hand, will automatically compute your well sizes given the starting well size and a dilution factor. While these are both useful, regular users may prefer the convenience of pasting data in bulk or uploading it from a text file. To use this feature, format your text such that each row has three numbers: the well size (# cells), the number of replicates for this size, and the number of positive outcomes for this size. The upload/paste feature also allows you input data for multiple patients. In this mode, the app will produce a graph showing the infection frequencies (IUPM) across the set of patients.